Team Lead Proposal


Tony Liang, Jeffrey Tang, Aditi Srinivasan, Sam Munn

University of British Columbia

2024-01-29

Background

Cytokines are small intercellular signalling protein that regulate immune responses by acting on various pathways

There are two types of cytokines (Type 1 or Type 2)1:

  • Type 1 favours the development of strong cellular immune responses
  • Type 2 favour a strong humoral immune response

Regulatory mechanisms in the context of cytokine induced signaling is well studied but there is limited ability to link back these cytokine induced activities on all gene expression activity partially due to short half-lives and pleiotropy2

Question/Hypothesis

  • What patterns of gene expression can be predicted from cytokine stimulation using bulk RNA sequencing data?

  • Other than the interleukin genes (IL-6, IL-10, IL-12, etc.), which other genes demonstrate a change in expression level when a cytokine response is triggered?

Figure 1: Network Approaches for Dissecting the Immune System1

Data Source

Retrieved from public database GEO1


Analysis Plan

How will you answer your main research question?

  • We propose performing differential expression analysis on a series of cytokine stimulated mice samples
  • Next we will perform enrichment analysis to see what genes are influenced by the cytokine-specific stimulant comparing this with control
  • We may propose some gene regulatory networks based on the relationships of genes and assess if the hub gene is the cytokine

Questions?

References

Hao Shi, Koon-Kiu Yan, Liang Ding, Chenxi Qian, Hongbo Chi, and Jiyang Yu. 2020. “Network Approaches for Dissecting the Immune System.” iScience 23 (8): 101354. https://doi.org/https://doi.org/10.1016/j.isci.2020.101354.
Lucey, Daniel R, Mario Clerici, and Gene M Shearer. 1996. “Type 1 and Type 2 Cytokine Dysregulation in Human Infectious, Neoplastic, and Inflammatory Diseases.” Clinical Microbiology Reviews 9 (4): 532–62.